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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ), 'gf_id' => 'HOM05D001397', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001397' ), 'data_identifier' => 'HOM05D001397', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001397', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '448', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21460' => 'bna', 'A06p04190' => 'bna', 'A06p07420' => 'bna', 'A08p04430' => 'bna', 'Aa31LG10G4800' => 'aar', 'Aa31LG10G6000' => 'aar', 'Aa31LG1G4300' => 'aar', 'Aa31LG5G8520' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.469' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.470__471' => 'aag', 'Actinidia01704' => 'ach', 'Actinidia08164' => 'ach', 'Actinidia15586' => 'ach', 'Actinidia18926' => 'ach', 'Actinidia35093' => 'ach', 'Actinidia40355' => 'ach', 'Ah.02g114980' => 'amhyb', 'Ah.04g154890' => 'amhyb', 'AL1G21450' => 'aly', 'AL1G55510' => 'aly', 'AL7G39000' => 'aly', 'Aqoxy2G02798' => 'aox', 'Aqoxy3G00256' => 'aox', 'Aqoxy3G02954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BB5XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4JWU9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5345PX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EDN8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7GLL8J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H36URW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5PABG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HL6MYD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMSN20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QWM1BH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U37EF8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN718F' => 'arhy', 'AT1G10600' => 'ath', 'AT1G48790' => 'ath', 'AT4G16144' => 'ath', 'ATR0706G159' => 'atr', 'ATR0730G168' => 'atr', 'ATR1125G122' => 'atr', 'Atru.chr11.2036' => 'acertr', 'Atru.chr4.2963' => 'acertr', 'Atru.chr9.866' => 'acertr', 'Atru.chr9.867' => 'acertr', 'AUR62005385' => 'cqu', 'AUR62014047' => 'cqu', 'AUR62016147' => 'cqu', 'AUR62029893' => 'cqu', 'AUR62033813' => 'cqu', 'AUR62035063' => 'cqu', 'AUR62042949' => 'cqu', 'AUR62043576' => 'cqu', 'BcaB04g17385' => 'bca', 'BcaB07g33717' => 'bca', 'BcaC05g24858' => 'bca', 'BcaC05g24949' => 'bca', 'BcaC06g32988' => 'bca', 'BcaC06g33463' => 'bca', 'BcaC06g33466' => 'bca', 'BcaC07g37103' => 'bca', 'BcaC08g43080' => 'bca', 'BcaC09g50306' => 'bca', 'BcaC09g50307' => 'bca', 'BcaNung00222' => 'bca', 'BolC1t02624H' => 'bol', 'BolC5t29640H' => 'bol', 'BolC6t35479H' => 'bol', 'BolC7t45292H' => 'bol', 'BolC8t47273H' => 'bol', 'BraA01t02050Z' => 'bra', 'BraA01t02051Z' => 'bra', 'BraA03t14059Z' => 'bra', 'BraA06t23624Z' => 'bra', 'BraA06t23946Z' => 'bra', 'BraA08t32470Z' => 'bra', 'C01p26800' => 'bna', 'C05p08920' => 'bna', 'C06p03390' => 'bna', 'C08p04720' => 'bna', 'CAN.G1425.19' => 'can', 'CAN.G1646.19' => 'can', 'CAN.G197.19' => 'can', 'CANSAT01G2164' => 'cansat', 'CARHR038760' => 'chi', 'CARHR222450' => 'chi', 'Carub.0001s1007' => 'cru', 'Carub.0001s3794' => 'cru', 'Carub.0007s2544' => 'cru', 'Ca_13994_v3' => 'car', 'Ca_17311_v3' => 'car', 'Ca_21458_v3' => 'car', 'Ca_25483_v3' => 'car', 'Ca_29724_v3' => 'car', 'Cc03_g01130' => 'ccan', 'Cc04_g07040' => 'ccan', 'Cc11_g15220' => 'ccan', 'CDE02G0485' => 'cde', 'CDE05G0898' => 'cde', 'CDE05G0925' => 'cde', 'CDE08G0034' => 'cde', 'CDE08G0660' => 'cde', 'CDE11G1190' => 'cde', 'Cfa009150' => 'cfa', 'Cfa015482' => 'cfa', 'Cfa019752' => 'cfa', 'Ciclev10004794m.g' => 'ccl', 'Ciclev10019782m.g' => 'ccl', 'Ciclev10032455m.g' => 'ccl', 'CiPaw.01G141800' => 'cil', 'CiPaw.02G076600' => 'cil', 'CiPaw.05G151500' => 'cil', 'CiPaw.15G131900' => 'cil', 'ClCG04G011040' => 'cla', 'ClCG04G011050' => 'cla', 'ClCG06G004740' => 'cla', 'COL.COLO4_04902' => 'col', 'COL.COLO4_34663' => 'col', 'Cpa.g.sc3.491' => 'cpa', 'Cpa.g.sc3.492' => 'cpa', 'Cpa.g.sc69.46' => 'cpa', 'Cpa.g.sc9.94' => 'cpa', 'Cre01.g024300' => 'cre', 'CsaV3_1G006690' => 'csa', 'CsaV3_6G022520' => 'csa', 'CsaV3_6G022530' => 'csa', 'CSS0013147' => 'camsi', 'CSS0021307' => 'camsi', 'CSS0046459' => 'camsi', 'CSS0047620' => 'camsi', 'CSS0047998' => 'camsi', 'DCAR_023210' => 'dca', 'DCAR_030481' => 'dca', 'DCAR_031105' => 'dca', 'Dinv02078' => 'din', 'Dinv15288' => 'din', 'Dinv15694' => 'din', 'Dinv28120' => 'din', 'Dinv44315' => 'din', 'Duzib052G0940' => 'dzi', 'Duzib068G1410' => 'dzi', 'Duzib084G0374' => 'dzi', 'Duzib151G1064' => 'dzi', 'Duzib205G0051' => 'dzi', 'Duzib251G0017' => 'dzi', 'Duzib268G0492' => 'dzi', 'ECA232G0992' => 'eca', 'ECA246G1757' => 'eca', 'EL10Ac2g02968' => 'bvu', 'EL10Ac3g04923' => 'bvu', 'EL10Ac5g11464' => 'bvu', 'EL10Ac6g13678' => 'bvu', 'EL10Ac6g14662' => 'bvu', 'Eucgr.B00736' => 'egr', 'Eucgr.B00739' => 'egr', 'Eucgr.B03319' => 'egr', 'Eucgr.H04029' => 'egr', 'FAN04G3249' => 'fan', 'FAN07G0371' => 'fan', 'FAN07G0820' => 'fan', 'FAN08G0205' => 'fan', 'FAN12G0297' => 'fan', 'FAN12G1650' => 'fan', 'FAN12G1942' => 'fan', 'FAN12G4322' => 'fan', 'FAN13G1855' => 'fan', 'FAN17G2622' => 'fan', 'FAN18G0529' => 'fan', 'FAN18G0659' => 'fan', 'FAN22G1542' => 'fan', 'FAN22G1955' => 'fan', 'FvH4_4g19320' => 'fve', 'FvH4_4g34380' => 'fve', 'FvH4_5g11880' => 'fve', 'Glyma.01G030400' => 'gma', 'Glyma.02G035100' => 'gma', 'Glyma.02G158000' => 'gma', 'Glyma.05G237800' => 'gma', 'Glyma.07G093100' => 'gma', 'Glyma.07G242500' => 'gma', 'Glyma.08G044900' => 'gma', 'Glyma.09G183100' => 'gma', 'Glyma.17G031700' => 'gma', 'Gohir.A03G139200' => 'ghi', 'Gohir.A09G064600' => 'ghi', 'Gohir.A09G176700' => 'ghi', 'Gohir.A10G168200' => 'ghi', 'Gohir.A11G005200' => 'ghi', 'Gohir.D02G162100' => 'ghi', 'Gohir.D09G063400' => 'ghi', 'Gohir.D09G172300' => 'ghi', 'Gohir.D10G174300' => 'ghi', 'Gohir.D11G004500' => 'ghi', 'Gorai.005G182100' => 'gra', 'Gorai.006G078500' => 'gra', 'Gorai.006G194200' => 'gra', 'Gorai.007G005500' => 'gra', 'Gorai.011G195000' => 'gra', 'GSVIVG01008310001' => 'vvi', 'GSVIVG01008314001' => 'vvi', 'GSVIVG01013737001' => 'vvi', 'GSVIVG01035040001' => 'vvi', 'HanXRQChr12g0354231' => 'han', 'HanXRQChr12g0383511' => 'han', 'HanXRQChr17g0552091' => 'han', 'Haze_01083' => 'cav', 'Haze_12184' => 'cav', 'Haze_18699' => 'cav', 'Hma1.2p1_0013F.1_g008900' => 'hma', 'Hma1.2p1_0399F.1_g143980' => 'hma', 'Hma1.2p1_0536F.1_g174010' => 'hma', 'Hma1.2p1_0653F.1_g196180' => 'hma', 'HPP92_004802' => 'vpl', 'HPP92_017240' => 'vpl', 'HPP92_026099' => 'vpl', 'HPP92_027568' => 'vpl', 'Hund02382' => 'sun', 'Hund02956' => 'sun', 'Hund03098' => 'sun', 'Hund25354' => 'sun', 'Lalb_Chr05g0216871' => 'lal', 'Lalb_Chr05g0222421' => 'lal', 'Lalb_Chr07g0182151' => 'lal', 'Lalb_Chr07g0182161' => 'lal', 'Lalb_Chr12g0200971' => 'lal', 'Lj2g0009923' => 'lja', 'Lj2g0010503' => 'lja', 'Lj3A1053T39' => 'lonja', 'Lj3A827G68' => 'lonja', 'Lj4g0024053' => 'lja', 'Lj5C150G9' => 'lonja', 'Lj9A425G47' => 'lonja', 'Lsat_1_v5_gn_1_44040' => 'lsa', 'Lsat_1_v5_gn_4_5661' => 'lsa', 'Lsat_1_v5_gn_5_53700' => 'lsa', 'Lsat_1_v5_gn_8_144760' => 'lsa', 'Manes.03G201800' => 'mes', 'Manes.05G114700' => 'mes', 'Manes.12G028300' => 'mes', 'Manes.15G006500' => 'mes', 'Mapoly0179s0015' => 'mpo', 'MBI09_g35837_MAGBIO' => 'mbi', 'MBI16_g05564_MAGBIO' => 'mbi', 'MBI18_g09590_MAGBIO' => 'mbi', 'MBI18_g28464_MAGBIO' => 'mbi', 'MBI18_g34963_MAGBIO' => 'mbi', 'MBI19_g18111_MAGBIO' => 'mbi', 'MBI19_g18112_MAGBIO' => 'mbi', 'MBI19_g37504_MAGBIO' => 'mbi', 'MBI19_g45472_MAGBIO' => 'mbi', 'MD06G1217700' => 'mdo', 'MD13G1092600' => 'mdo', 'MD13G1157700' => 'mdo', 'MD14G1227900' => 'mdo', 'MD16G1093400' => 'mdo', 'MD16G1158700' => 'mdo', 'Medtr4g121470' => 'mtr', 'Medtr5g034240' => 'mtr', 'Medtr6g083940' => 'mtr', 'Medtr6g083950' => 'mtr', 'Medtr8g104310' => 'mtr', 'MELO3C002093.2' => 'cme', 'MELO3C021283.2' => 'cme', 'Migut.E01769' => 'egut', 'Migut.G00100' => 'egut', 'Migut.G00102' => 'egut', 'Migut.N00055' => 'egut', 'MSTRG.3870' => 'ama', 'MSTRG.589' => 'ama', 'MSTRG.9565' => 'ama', 'Nitab4.5_0000169g0060' => 'nta', 'Nitab4.5_0000884g0120' => 'nta', 'Nitab4.5_0002906g0090' => 'nta', 'Nitab4.5_0003433g0070' => 'nta', 'Nitab4.5_0005333g0020' => 'nta', 'Nn3g17890' => 'nnu', 'Nn3g21641' => 'nnu', 'Nn4g22772' => 'nnu', 'Nn4g25646' => 'nnu', 'Oeu032969.1' => 'oeu', 'Oeu046563.1' => 'oeu', 'Os01g0338200' => 'osa', 'Os01g0499300' => 'osa', 'Os01g0661500' => 'osa', 'Peaxi162Scf00065g00324' => 'pax', 'Peaxi162Scf00683g00022' => 'pax', 'PGR004G0959' => 'pgr', 'PGR083G0583' => 'pgr', 'PGR102G2285' => 'pgr', 'PGSC0003DMG400005643' => 'stu', 'PGSC0003DMG400007555' => 'stu', 'PGSC0003DMG402009742' => 'stu', 'Phvul.002G071100' => 'pvu', 'Phvul.002G317500' => 'pvu', 'Phvul.003G111000' => 'pvu', 'Phvul.004G156088' => 'pvu', 'Potri.010G041200' => 'ptr', 'Potri.010G141100' => 'ptr', 'Potri.015G045800' => 'ptr', 'Pp3c11_14050' => 'ppa', 'Pp3c13_4580' => 'ppa', 'Pp3c17_10020' => 'ppa', 'Pp3c5_10200' => 'ppa', 'Pp3c6_16700' => 'ppa', 'PRCOL_00007236' => 'pco', 'Prupe.1G125200' => 'ppe', 'Prupe.1G253200' => 'ppe', 'Prupe.5G222900' => 'ppe', 'Psat1g036960' => 'psa', 'Psat2g103120' => 'psa', 'Psat4g023200' => 'psa', 'Psat7g008440' => 'psa', 'PSO017G3250' => 'pso', 'PSO063G2777' => 'pso', 'PSO170G2044' => 'pso', 'PSO210G5422' => 'pso', 'PSO339G6336' => 'pso', 'PSO384G1639' => 'pso', 'PSO478G4193' => 'pso', 'PSO541G1200' => 'pso', 'PSO761G0705' => 'pso', 'PSO832G2672' => 'pso', 'QL03p060200' => 'qlo', 'QL06p011440' => 'qlo', 'QL10p025680' => 'qlo', 'RcHm_v2.0_Chr4g0424341' => 'rch', 'RcHm_v2.0_Chr4g0443791' => 'rch', 'RcHm_v2.0_Chr7g0185701' => 'rch', 'Rhsim04G0232600' => 'rsi', 'Rhsim08G0132000' => 'rsi', 'Rhsim12G0046300' => 'rsi', 'Sabra10G0026100' => 'sbr', 'Sabra10G0109100' => 'sbr', 'Sabra15G0039700' => 'sbr', 'SalBow1G5116' => 'sbo', 'SalBow8G1738' => 'sbo', 'SalBow8G3812' => 'sbo', 'Sc10g0009360' => 'sci', 'Sc10g0009370' => 'sci', 'Sc10g0009420' => 'sci', 'Sc13g0006310' => 'sci', 'Sc14g0008640' => 'sci', 'Sed0012111' => 'sed', 'Sed0021143' => 'sed', 'Sed0027940' => 'sed', 'SEGI_01432' => 'sgi', 'SEGI_09744' => 'sgi', 'SEGI_28241' => 'sgi', 'SGA_v2.0_scaffold107G30795' => 'sas', 'SGA_v2.0_scaffold18G08385' => 'sas', 'SGA_v2.0_scaffold42G16020' => 'sas', 'SHI00160' => 'shi', 'SHI00161' => 'shi', 'SHI07298' => 'shi', 'SHI15035' => 'shi', 'SHI15789' => 'shi', 'SHI19669' => 'shi', 'SHI19779' => 'shi', 'SHI20054' => 'shi', 'SHI20171' => 'shi', 'SHI20172' => 'shi', 'SHI24227' => 'shi', 'SHI31571' => 'shi', 'SHI31572' => 'shi', 'SHI31760' => 'shi', 'SHI32991' => 'shi', 'SHI32992' => 'shi', 'SHI33866' => 'shi', 'SHI33868' => 'shi', 'SHI34395' => 'shi', 'SHI34397' => 'shi', 'SHI34510' => 'shi', 'SHI34511' => 'shi', 'SHI34512' => 'shi', 'SHI35733' => 'shi', 'SHI35735' => 'shi', 'SHI35898' => 'shi', 'SHI36252' => 'shi', 'SHI36673' => 'shi', 'SHI37428' => 'shi', 'SHI37429' => 'shi', 'SHI37480' => 'shi', 'SHI43891' => 'shi', 'SHI46398' => 'shi', 'SHI47288' => 'shi', 'SHI47949' => 'shi', 'SHI48680' => 'shi', 'SHI49084' => 'shi', 'SHI52608' => 'shi', 'SHI53446' => 'shi', 'SHI53785' => 'shi', 'SHI53801' => 'shi', 'SHI53984' => 'shi', 'SHI54312' => 'shi', 'SHI54389' => 'shi', 'SHI54459' => 'shi', 'SHI54643' => 'shi', 'SHI54797' => 'shi', 'SHI54913' => 'shi', 'SHI55006' => 'shi', 'SHI55132' => 'shi', 'SHI55156' => 'shi', 'SMO010G0022' => 'smo', 'SMO328G0038' => 'smo', 'SMO356G0165' => 'smo', 'Solyc01g060280.4' => 'sly', 'Solyc03g119330.3' => 'sly', 'Sopen01g026500' => 'spe', 'Sopen03g038200' => 'spe', 'Sp1g09280' => 'spa', 'Sp1g35710' => 'spa', 'Sp7g14630' => 'spa', 'TAR362G0524' => 'tar', 'TAR374G1228' => 'tar', 'TAR374G1335' => 'tar', 'THA.LOC104820389' => 'tha', 'THA.LOC104821797' => 'tha', 'THA.LOC104823645' => 'tha', 'Thecc.02G250800' => 'tca', 'Thecc.03G037300' => 'tca', 'Thecc.04G295800' => 'tca', 'Thhalv10008718m.g' => 'esa', 'Thhalv10011406m.g' => 'esa', 'Thhalv10025009m.g' => 'esa', 'TPR.G15170' => 'tpr', 'TPR.G16832' => 'tpr', 'TPR.G21089' => 'tpr', 'TPR.G25945' => 'tpr', 'TPR.G30967' => 'tpr', 'TPR.G32672' => 'tpr', 'TWI36G0674' => 'twi', 'TWI53G0938' => 'twi', 'TWI73G0765' => 'twi', 'TWI81G0493' => 'twi', 'unitig_21.g20426' => 'ugi', 'unitig_32.g10636' => 'ugi', 'vmacro01169' => 'vma', 'vmacro08073' => 'vma', 'vmacro17707' => 'vma', 'VMungo0251G0016' => 'vmu', 'VMungo0464G1324' => 'vmu', 'VMungo1215G1129' => 'vmu', 'VMungo1215G3354' => 'vmu', 'Zm00001eb131320' => 'zma', 'Zm00001eb340870' => 'zma', 'Zm00001eb341740' => 'zma', 'Zm00001eb359600' => 'zma' ) $gf_id = 'HOM05D001397' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001397' ) $data_identifier = 'HOM05D001397' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 3, 'shi' => (int) 51, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359600' $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